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- PDB-7an8: Enzyme of biosynthetic pathway -

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Basic information

Entry
Database: PDB / ID: 7an8
TitleEnzyme of biosynthetic pathway
ComponentsChorismate dehydratase
KeywordsBIOSYNTHETIC PROTEIN / Enzyme activity / Biosynthetic pathway
Function / homologychorismate dehydratase / Chorismate dehydratase / Menaquinone biosynthesis enzyme / Menaquinone biosynthesis / menaquinone biosynthetic process / hydro-lyase activity / 3-[(1-Carboxyvinyl)oxy]benzoic acid / Chorismate dehydratase
Function and homology information
Biological speciesStreptomyces coelicolor A3
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.01 Å
AuthorsArchna, A. / Breithaupt, C. / Stubbs, M.T.
Funding support Germany, 1items
OrganizationGrant numberCountry
European Regional Development Fund Germany
CitationJournal: J.Biol.Chem. / Year: 2022
Title: Mechanism of chorismate dehydratase MqnA, the first enzyme of the futalosine pathway, proceeds via substrate-assisted catalysis
Authors: Prasad, A. / Breithaupt, C. / Nguyen, D.A. / Lilie, H. / Ziegler, J. / Stubbs, M.T.
History
DepositionOct 11, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Oct 26, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chorismate dehydratase
B: Chorismate dehydratase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5995
Polymers65,0902
Non-polymers5083
Water5,999333
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2570 Å2
ΔGint-7 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.956, 95.075, 72.137
Angle α, β, γ (deg.)90.000, 93.960, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 1 through 155 or resid 157 through 203 or resid 205 through 283 or resid 302))
21(chain B and (resid 1 through 155 or resid 157 through 203 or resid 205 through 283 or resid 402))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resid 1 through 155 or resid 157 through 203 or resid 205 through 283 or resid 302))A1 - 155
121(chain A and (resid 1 through 155 or resid 157 through 203 or resid 205 through 283 or resid 302))A157 - 203
131(chain A and (resid 1 through 155 or resid 157 through 203 or resid 205 through 283 or resid 302))A205 - 283
141(chain A and (resid 1 through 155 or resid 157 through 203 or resid 205 through 283 or resid 302))A302
211(chain B and (resid 1 through 155 or resid 157 through 203 or resid 205 through 283 or resid 402))B1 - 155
221(chain B and (resid 1 through 155 or resid 157 through 203 or resid 205 through 283 or resid 402))B157 - 203
231(chain B and (resid 1 through 155 or resid 157 through 203 or resid 205 through 283 or resid 402))B205 - 283
241(chain B and (resid 1 through 155 or resid 157 through 203 or resid 205 through 283 or resid 402))B402

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Components

#1: Protein Chorismate dehydratase / Menaquinone biosynthetic enzyme MqnA


Mass: 32545.057 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coelicolor A3(2) (bacteria)
Gene: mqnA, SCO4506 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9L0T8, chorismate dehydratase
#2: Chemical ChemComp-RDH / 3-[(1-Carboxyvinyl)oxy]benzoic acid / 3-(3-oxidanyl-3-oxidanylidene-prop-1-en-2-yl)oxybenzoic acid


Mass: 208.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H8O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 333 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.36 Å3/Da / Density % sol: 47.94 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18 mM MES Sodium Salt, 4.5% v/v 2-Propanol, 25% w/v PEG 4000, 10% v/v Glycerol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Dec 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.01→47.54 Å / Num. obs: 73407 / % possible obs: 93.2 % / Redundancy: 1.901 % / Biso Wilson estimate: 28.972 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.136 / Χ2: 0.978 / Net I/σ(I): 6.69
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
2.01-2.141.6390.5291.6698240.730.72476.9
2.14-2.281.9370.4062.35112540.8080.55894.4
2.28-2.471.940.2943.07106060.8850.40595.3
2.47-2.71.940.2024.1398620.9430.27896.1
2.7-3.021.9410.1355.8690330.9690.18697.3
3.02-3.481.9390.0739.8780030.9890.197.8
3.48-4.261.9440.04714.8667330.9940.06597.9
4.26-61.9520.03916.8552380.9960.05497.6
6-101.9510.03219.1228540.9970.04595.7

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.17.1refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7AHR

7ahr


Resolution: 2.01→47.54 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2352 1946 5 %
Rwork0.2088 36957 -
obs0.2101 38903 97.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 58.79 Å2 / Biso mean: 26.5252 Å2 / Biso min: 12.82 Å2
Refinement stepCycle: final / Resolution: 2.01→47.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4449 0 36 333 4818
Biso mean--24.45 28.65 -
Num. residues----568
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A2694X-RAY DIFFRACTION5.618TORSIONAL
12B2694X-RAY DIFFRACTION5.618TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.01-2.070.43011080.3242205976
2.07-2.120.29881300.2936245791
2.12-2.180.2581400.2794266899
2.18-2.250.3171430.2562271199
2.25-2.330.29441400.2494266699
2.33-2.430.25481420.24322693100
2.43-2.540.28731410.2394267799
2.54-2.670.25531430.2332720100
2.67-2.840.28471420.22732702100
2.84-3.060.25761420.21442694100
3.06-3.370.20231420.20122701100
3.37-3.850.24381440.1732729100

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